The findings mark the first time a domestic inquiry has said there is evidence the army committed war crimes, and are all the more remarkable given that the report was commissioned by Mahinda Rajapaksa.
Sri Lanka's former strongman leader oversaw the final push against Tamil Tiger rebels in 2009 before losing power in January, and has always fiercely denied his troops committed war crimes.
He ordered the inquiry in 2013 in a bid to deflect mounting international censure, and the new government made the findings public in line with a promise to the UN Human Rights Council last month.
"There are credible allegations which, if proved to the required standard, may show that some members of the armed forces committed acts during the final phase of the war that amounted to war crimes giving rise to individual criminal responsibility," said the 178-page report presented to parliament today.
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The government of Rajapaksa's successor, Maithripala Sirisena, has vowed to punish war criminals and set up a truth commission and a reparations office to help heal the wounds left by the conflict.
The latest inquiry was overseen by retired judge Maxwell Paranagama and examined claims in a documentary broadcast by Britain's Channel 4 that purportedly showed Sri Lankan soldiers executing Tamil prisoners.
At the time Sri Lanka's military dismissed the documentary, "No Fire Zone: Sri Lanka Killing Fields", as a fabrication.
But Paranagama concluded there was evidence to suggest the footage -- showing prisoners stripped naked and blindfolded, their arms tied behind their backs, being shot dead by mocking soldiers -- was genuine.
It said another high-profile case involving the execution of the top Tamil Tiger political leadership on or about May 18, 2009 should also be probed by an independent judicial inquiry despite the then-government denying the killings.